# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.t06.alpha.rdb (weight 0.659012) # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.alpha.rdb (weight 0.659012) # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2231 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2231 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0316.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2231 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2231 # # ============================================ # Comments from T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1900 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1900 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1900 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1900 # # ============================================ # Comments from T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0316.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 329 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0316.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 329 # # ============================================ # Comments from T0316.t2k.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0316.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 23.7232 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0316.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 329 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1159 0.0446 0.8394 2 S 0.1336 0.0388 0.8276 3 D 0.0956 0.0789 0.8256 4 N 0.0587 0.1592 0.7821 5 S 0.0369 0.1664 0.7967 6 K 0.0879 0.0531 0.8590 7 T 0.2715 0.0186 0.7099 8 R 0.7373 0.0049 0.2578 9 V 0.9192 0.0032 0.0776 10 V 0.9309 0.0032 0.0659 11 V 0.9284 0.0034 0.0682 12 G 0.9042 0.0042 0.0917 13 M 0.7320 0.0220 0.2459 14 S 0.3272 0.0264 0.6464 15 G 0.1050 0.0604 0.8346 16 G 0.0966 0.1382 0.7652 17 V 0.0659 0.5680 0.3661 18 D 0.0173 0.7937 0.1890 19 S 0.0052 0.9370 0.0578 20 S 0.0048 0.9561 0.0391 21 V 0.0047 0.9599 0.0354 22 T 0.0047 0.9600 0.0353 23 A 0.0047 0.9600 0.0353 24 L 0.0047 0.9608 0.0345 25 L 0.0047 0.9592 0.0361 26 L 0.0047 0.9573 0.0380 27 K 0.0049 0.9502 0.0449 28 E 0.0055 0.9198 0.0747 29 Q 0.0407 0.4620 0.4973 30 G 0.0373 0.0294 0.9332 31 Y 0.0942 0.0144 0.8913 32 D 0.5010 0.0114 0.4875 33 V 0.8435 0.0045 0.1519 34 I 0.8356 0.0312 0.1333 35 G 0.8878 0.0096 0.1026 36 I 0.9122 0.0057 0.0821 37 F 0.8840 0.0135 0.1025 38 M 0.7729 0.0368 0.1904 39 K 0.6431 0.0464 0.3106 40 N 0.4848 0.0456 0.4696 41 W 0.3187 0.0648 0.6166 42 D 0.2037 0.0829 0.7134 43 D 0.1162 0.1294 0.7544 44 T 0.0683 0.1381 0.7937 45 D 0.0623 0.1520 0.7857 46 E 0.0630 0.1414 0.7956 47 N 0.0736 0.1103 0.8161 48 G 0.0911 0.0839 0.8250 49 V 0.1874 0.0821 0.7304 50 C 0.3213 0.0800 0.5987 51 T 0.1768 0.1235 0.6997 52 A 0.0952 0.2173 0.6874 53 T 0.0339 0.5548 0.4113 54 E 0.0255 0.5677 0.4069 55 D 0.0352 0.5705 0.3944 56 Y 0.0081 0.8878 0.1041 57 K 0.0049 0.9406 0.0544 58 D 0.0048 0.9491 0.0460 59 V 0.0047 0.9591 0.0362 60 V 0.0047 0.9604 0.0349 61 A 0.0047 0.9604 0.0350 62 V 0.0047 0.9596 0.0357 63 A 0.0047 0.9580 0.0373 64 D 0.0053 0.9453 0.0494 65 Q 0.0069 0.9002 0.0929 66 I 0.0472 0.5317 0.4211 67 G 0.0506 0.0173 0.9321 68 I 0.0677 0.0082 0.9241 69 P 0.1665 0.0135 0.8200 70 Y 0.7347 0.0092 0.2560 71 Y 0.8986 0.0069 0.0946 72 S 0.9151 0.0056 0.0793 73 V 0.8512 0.0113 0.1375 74 N 0.5772 0.0149 0.4079 75 F 0.0598 0.4456 0.4946 76 E 0.0131 0.7186 0.2683 77 K 0.0066 0.8909 0.1025 78 E 0.0069 0.9109 0.0822 79 Y 0.0089 0.8877 0.1033 80 W 0.0061 0.9129 0.0810 81 D 0.0072 0.9094 0.0834 82 R 0.0090 0.8725 0.1185 83 V 0.0137 0.8735 0.1128 84 F 0.0075 0.8994 0.0931 85 E 0.0055 0.9441 0.0504 86 Y 0.0047 0.9510 0.0443 87 F 0.0048 0.9528 0.0424 88 L 0.0048 0.9534 0.0419 89 A 0.0048 0.9554 0.0398 90 E 0.0053 0.9520 0.0427 91 Y 0.0082 0.9359 0.0559 92 R 0.0082 0.8981 0.0937 93 A 0.0339 0.5376 0.4284 94 G 0.0293 0.1719 0.7989 95 R 0.0632 0.0458 0.8910 96 T 0.0776 0.0243 0.8982 97 P 0.0759 0.0387 0.8854 98 N 0.0964 0.0380 0.8656 99 P 0.1109 0.1306 0.7585 100 D 0.2102 0.1829 0.6068 101 V 0.2842 0.2575 0.4583 102 M 0.2712 0.2326 0.4962 103 C 0.1438 0.2765 0.5798 104 N 0.0787 0.2129 0.7084 105 K 0.0505 0.4132 0.5363 106 E 0.1470 0.4321 0.4209 107 I 0.2941 0.3511 0.3548 108 K 0.2752 0.3413 0.3835 109 F 0.0288 0.8330 0.1382 110 K 0.0071 0.9192 0.0737 111 A 0.0064 0.9215 0.0722 112 F 0.0058 0.9403 0.0539 113 L 0.0054 0.9508 0.0438 114 D 0.0051 0.9529 0.0420 115 Y 0.0050 0.9513 0.0437 116 A 0.0051 0.9474 0.0475 117 I 0.0052 0.9390 0.0558 118 T 0.0061 0.8966 0.0973 119 L 0.0442 0.4757 0.4801 120 G 0.0497 0.0269 0.9234 121 A 0.1020 0.0123 0.8857 122 D 0.2563 0.0534 0.6903 123 Y 0.8920 0.0109 0.0971 124 V 0.9133 0.0068 0.0800 125 A 0.8795 0.0085 0.1120 126 T 0.6904 0.0203 0.2893 127 G 0.3570 0.0362 0.6068 128 H 0.3539 0.0914 0.5547 129 Y 0.5461 0.1271 0.3268 130 A 0.6971 0.1196 0.1833 131 R 0.7657 0.0644 0.1699 132 V 0.8198 0.0264 0.1538 133 A 0.7825 0.0169 0.2006 134 R 0.7334 0.0219 0.2447 135 D 0.3001 0.0430 0.6569 136 E 0.0541 0.0868 0.8591 137 D 0.0526 0.0420 0.9054 138 G 0.0748 0.0386 0.8866 139 T 0.4150 0.0141 0.5709 140 V 0.8384 0.0053 0.1563 141 H 0.8773 0.0087 0.1140 142 M 0.8987 0.0073 0.0941 143 L 0.8357 0.0207 0.1436 144 R 0.7976 0.0160 0.1864 145 G 0.6077 0.0331 0.3592 146 V 0.3890 0.0455 0.5655 147 D 0.2189 0.0412 0.7399 148 N 0.0328 0.2029 0.7642 149 G 0.0447 0.1681 0.7873 150 K 0.0787 0.2145 0.7068 151 D 0.1860 0.1867 0.6272 152 Q 0.2792 0.3651 0.3556 153 T 0.4367 0.3796 0.1837 154 Y 0.4300 0.4431 0.1270 155 F 0.3589 0.4965 0.1446 156 L 0.2552 0.5085 0.2362 157 S 0.1666 0.4501 0.3833 158 Q 0.1212 0.3451 0.5337 159 L 0.1528 0.1150 0.7322 160 S 0.0955 0.0741 0.8304 161 Q 0.0062 0.8738 0.1200 162 E 0.0054 0.8938 0.1008 163 Q 0.0065 0.8946 0.0990 164 L 0.0092 0.8910 0.0998 165 Q 0.0080 0.8443 0.1477 166 K 0.0116 0.7528 0.2356 167 T 0.0470 0.6057 0.3473 168 M 0.0961 0.3321 0.5718 169 F 0.0924 0.1565 0.7511 170 P 0.0837 0.1609 0.7554 171 L 0.0501 0.3082 0.6417 172 G 0.0417 0.2607 0.6976 173 H 0.0407 0.3186 0.6407 174 L 0.0901 0.2212 0.6886 175 E 0.0965 0.1890 0.7145 176 K 0.0502 0.5586 0.3913 177 P 0.0122 0.8586 0.1292 178 E 0.0118 0.9057 0.0825 179 V 0.0143 0.9111 0.0745 180 R 0.0160 0.8963 0.0877 181 R 0.0254 0.8011 0.1736 182 L 0.0254 0.6971 0.2775 183 A 0.0270 0.2890 0.6840